Researchers in Hong Kong have found that the reaction of the body's immune system may be a key factor.
They believe that the deaths associated with so-called killer strains of flu may in fact have been caused by the immune system itself.
The finding could help scientists to develop effective treatments for future strains of the virus.
Experts warned recently that the virus is constantly mutating and a virulent strain could emerge at any time.
The last major flu pandemic in 1918 killed tens of millions of people in Europe alone. An outbreak in Hong Kong in 1997 killed 18 people.
Immune response
Researchers at the University of Hong Kong examined that strain in a laboratory.
They found that it triggered a very strong immune response. This produced high levels of cytokines, which enable the body to kill harmful cells.
However, the researchers believe that so many of the cytokines were triggered that they started to attack the body's own cells and cause multi-organ failure.
This goes against previous theories that the virus itself is responsible for deaths.
Writing in The Lancet, the researchers warned that another flu pandemic "is a certainty".
But they added that their findings could help to develop treatments to fight any new strain.
"[It] will help us to be better prepared for the next influenza pandemic," they wrote.
Strong data
Wendy Barclay, a lecturer in microbiology at the University of Reading, backed the findings.
"It is fairly well accepted that many diseases have an immune pathology. The data in this study is very strong."
But speaking to BBC News Online, she suggested scientists need to be careful when developing drugs to tackle the immune system.
"The body has an immune system for a purpose. We need to be careful with any drugs that deal with the immune response.
"It is all about achieving a balance between the virus and host.
"If the body or host is producing too many cytokines, we may be able to prevent this by dampening down the response but we need to be careful that we don't also damage the host's ability to fight the virus."